Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
415
datasets available to search
ShareScore release 0.9.0
Dataset results
415 results for “incompletive”
Data from: Improved robustness to gene tree incompleteness, estimation errors, and systematic homology errors with weighted TREE-QMC
Open the record for dataset details and reuse information.
Data from: Quantifying and estimating ecological network diversity based on incomplete sampling data
Open the record for dataset details and reuse information.
Code and data from: A hierarchical approach for estimating state-specific mortality and state transition in dispersing animals with incomplete death records
Open the record for dataset details and reuse information.
Data from: Estimating diversification rates on incompletely-sampled phylogenies: theoretical concerns and practical solutions
<p>Molecular phylogenies are a key source of information about the tempo and mode of species diversification. However, most empirical phylogenies do not contain representatives of all species, such that diversification rates are typically estimated from incompletely sampled data. Most researchers recognize that incomplete sampling can lead to biased rate estimates, but the statistical properties of methods for accommodating incomplete sampling remain poorly known. In this point of view, we demonstrate theoretical concerns with the widespread use of analytical sampling corrections for sparsely sampled phylogenies of higher taxonomic groups. In particular, corrections based on "sampling fractions" can lead to low statistical power to infer rate variation when it is present, depending on the likelihood function used for inference. In the extreme, the sampling fraction correction can lead to spurious patterns of diversification that are driven solely by unbalanced sampling across the tree in concert with low overall power to infer shifts. Stochastic polytomy resolution provides an alternative to sampling fraction approaches that avoids some of these biases. We show that stochastic polytomy resolvers can greatly improve the power of common analyses to estimate shifts in diversification rates. We introduce a new stochastic polytomy resolution method (TACT: Taxonomic Addition for Complete Trees) that uses birth-death-sampling estimators across an ultrametric phylogeny to estimate branching times for unsampled taxa, with taxonomic information to compatibly place new taxa onto a backbone phylogeny. We close with practical recommendations for diversification inference under several common scenarios of incomplete sampling.</p>
Data from: Incomplete host immunity favors the evolution of virulence in an emergent pathogen
Immune memory evolved to protect hosts from reinfection, but incomplete responses that allow future reinfection might inadvertently select for more harmful pathogens. We present empirical and modeling evidence that incomplete immunity promotes the evolution of higher virulence in a natural host-pathogen system. We performed sequential infections of house finches with Mycoplasma gallisepticum strains of varying virulence. Virulent bacterial strains generated stronger host protection against reinfection than less virulent strains, and thus excluded less virulent strains from infecting previously-exposed hosts. In a two-strain model, the resulting fitness advantage selected for an almost two-fold increase in pathogen virulence. Thus, the same immune systems that protect hosts from infection can concomitantly drive the evolution of more harmful pathogens in nature.
Sol Lewitt - Incomplete Open Cube 6/8 (1974)
Painted aluminum, 106.7 x 106.7 x 106.7 cm Solomon R. Guggenheim Foundation, Hannelore B. and Rudolph B. Schulhof Collection, bequest of Hannelore B. Schulhof, 2012 © Sol LeWitt, by SIAE 2012 Source: Objaverse 1.0 / Sketchfab
Learning stochastic process-based models of dynamical systems from knowledge and data - Libraries, incomplete models and data
<p>The archive contains all libraries of domain knowledge, the incomplete models and the data used in the experiments described in the manuscript titled "Learning stochastic process-based models of dynamical systems from knowledge and data" pubilshed in BMC Systems Biology</p>
Incomplete human male cranium
An image-based 3D model of an incomplete human cranium created from 340 overlapping images in Agisoft PhotoScan using settings for medium quality. Source: Objaverse 1.0 / Sketchfab
All-atom molecular dynamics simulations of incomplete ATP synthase rotor rings with unusually high stoichiometry predicted by the AlphaFold2-based method
<p>The trajectories of all-atom MD simulations of <span>AlphaFold2 4, 11, 16 or 18-mer structures of the subunit <em>c</em> from<br></span><span><em>Candidatus Kryptonium thompsoni</em></span><span> (CKt_Nmer_lipid_mix_CHM36m_303K_500ns) and <br></span><span><em>Thalassoglobus polymorphus </em>(Tp_Nmer_lipid_mix_CHM36m_303K_500ns), and <br>AlphaFold2 11-mer structure of the subunit <em>c</em> from <em>Spinacia oleracea</em> (So_11mer-c20_POPC_CHM36m_303K_300ns) </span><span>in a lipid bilayer.</span></p> <p><span>Simulations have been performed using the CHARMM36m force field, running with the GROMACS 2022 package.</span></p>
Dataset from: Incomplete lineage sorting and reticulate evolution mask species relationships in Brunelliaceae, an Andean family with rapid, recent diversification
<p><strong>Premise</strong>: To date, phylogenetic relationships within the monogeneric Brunelliaceae have been based on morphological evidence, which does not provide sufficient phylogenetic resolution. Here we use target-enriched nuclear data to improve our understanding of phylogenetic relationships in the family. </p> <p><strong>Methods</strong>: We used the Angiosperms353 toolkit for targeted recovery of exonic regions and supercontigs (exons + introns) from low copy nuclear genes from 53 of 70 species in <em>Brunellia</em>, and several outgroup taxa. We removed loci that indicated biased relationships and applied concatenated and coalescent methods to infer <em>Brunellia</em> phylogeny. We identified conflicts among gene trees that may reflect hybridization or incomplete lineage-sorting events and assessed their impact on the phylogeny. Finally, we performed ancestral-state reconstructions of morphological traits and assessed the homology of character states used to define sections and subsections in <em>Brunellia</em>.</p> <p><strong>Results</strong>: <em>Brunellia</em> comprises two major clades and several subclades. Most of these clades/subclades do not correspond to previous infrageneric taxa. There is high topological incongruence among the subclades across analyses.</p> <p><strong>Conclusions</strong>: Phylogenetic reconstructions point to rapid species diversification in Brunelliaceae, reflected in very short branches between successive species splits. The removal of putatively biased loci slightly improves phylogenetic support for individual clades. Reticulate evolution due to hybridization and/or incomplete lineage sorting likely both contribute to gene-tree discordance. Morphological characters used to define taxa in current classification schemes are homoplastic in the ancestral character state reconstructions. While target enrichment data allows us to broaden our understanding of diversification in <em>Brunellia</em>, the relationships among subclades remain incompletely understood.</p>
Wmid-42fe18 - Incomplete skirted terret ring
An incomplete harness fitting: skirted terret type of Roman (AD mid-1st century and mid-2nd century) dating. Less than 50% of the terret ring is present, with most of the ring missing and part of the skirt being incomplete. The upper loop is incomplete with a flat cross section. The base of the loop expands and in width and sits on an integral skirt. The skirt on such terret rings are normally lozenge shape in plan with the two terminal corners being upturned, and the side corners are downturned, neither of these terminal corners are present. The edges of the break are patinated. The underside of the skirt is hollow but protruding from each terminal there is a rectangular loop which is oval in section. For more information, please visit the online database record available at: https://finds.org.uk/database/artefacts/record/id/1059824 Source: Objaverse 1.0 / Sketchfab
Wmid-8156c5 2020t112 - Incomplete saxon brooch
A gilded silver fragment of a cast object, possibly a bow brooch. The fragment comprises a jagged plate-like piece which slopes lightly downwards from a central ridge. The ridge is plain silver, is grooved and flares slightly at each end. The surviving areas flanking the ridge are gilded, and are decorated with a raised annulet within a ?semi-circular panel demarcated by a raised line. On the reverse is a raised rib, possibly the remains of a catch-plate, with remains of gilding. For more information, please visit the online database record available at: https://finds.org.uk/database/artefacts/record/id/991292 Source: Objaverse 1.0 / Sketchfab
Wmid-321fb6 - Incomplete medieval box mount
An incomplete copper alloy bar mount, probably from a casket, chest or box, of Medieval dating (c. AD 1200 to AD 1400). Less than 25% of the bar mount is present, consisting of one terminal and part of the bar. The terminal is a lis or lys shape, with a circular attachment hole placed centrally (2.9 mm) around diagonal side grooves.The surviving section of the bar mount has a raised area with bevelled sides, creating a pyramid type effect (11.4 mm by 8.6 mm). The underside is slightly concave along its length, with raised edges. The terminal is bent upwards at an angle of approx 45 degrees. Gilding is still present on the upper surfaces. For more detail, please visit the online database record available at: https://finds.org.uk/database/artefacts/record/id/1059761 Source: Objaverse 1.0 / Sketchfab
Wmid-5003d2 - Incomplete Middle Bronze Age spear
An incomplete copper alloy, tip from a spearhead, probably of Middle Bronze Age period, dating from c. BC 1500 to c. BC 1150. The object is broadly triangular in plan and broadly lozenge shaped in cross section. The object has a blunt point at the top, which seems to have sustained some damage. From the point the sides of the object taper out, ensuring the object is wider at the base. There is a central raised ridge running vertically down the middle of the spear head, this appears on both sides. There is an old horizontal break at the base of the object, probably indicating the spear was broken in antiquity. There are traces of small sides loops. There is damage to both edges of the blade. For more information, please visit the online database record available at: https://finds.org.uk/database/artefacts/record/id/1063942# Source: Objaverse 1.0 / Sketchfab
Phylogenomic discordance is driven by wide-spread introgression and incomplete lineage sorting during rapid species diversification within rattlesnakes (Viperidae: Crotalus and Sistrurus)
<p>Phylogenomics allows us to uncover the historical signal of evolutionary processes through time and estimate phylogenetic networks accounting for these signals. Insight from genome-wide data further allows us to pinpoint the contributions to phylogenetic signal from hybridization, introgression, and ancestral polymorphism across the genome. Here, we focus on how these processes have contributed to phylogenetic discordance among rattlesnakes (genera <em>Crotalus</em> and <em>Sistrurus</em>), a group for which there are numerous conflicting phylogenetic hypotheses based on a diverse array of molecular datasets and analytical methods. We address the instability of the rattlesnake phylogeny using genomic data generated from transcriptomes sampled from nearly all known species. These genomic data, analyzed with coalescent and network-based approaches, reveal numerous instances of rapid speciation where individual gene trees conflict with the species tree. Moreover, the evolutionary history of rattlesnakes is dominated by incomplete speciation and frequent hybridization, both of which have likely influenced past interpretations of phylogeny. We present a new framework in which the evolutionary relationships of this group can only be understood in light of genome-wide data and network-based analytical methods. Our data suggest that network radiations, like those seen within the rattlesnakes, can only be understood in a phylogenomic context, necessitating similar approaches in our attempts to understand evolutionary history in other rapidly radiating species.</p> <p>La filogenómica nos permite descubrir la señal histórica de los procesos evolutivos a través del tiempo y estimar redes filogenéticas tomando en cuenta estas señales. El conocimiento de datos genómicos incluso permiten distinguir la contribución de la señal filogenética de la hibridación, introgresión, y de polimorfismos ancestrales a lo largo del genoma. En este trabajo nos enfocamos en como estos procesos han contribuido a la discordancia filogenética entre las serpientes de cascabel, un grupo en el que hay numerosos conflictos en las hipótesis filogenéticas obtenidas de un grupo variado de datos moleculares y métodos analíticos. Nosotros abordamos la inestabilidad de la filogenia de las serpientes de cascabel (generos <em>Crotalus</em> y <em>Sistrurus</em>) usando datos genómicos generados de transcriptomas muestreados en la mayoría de las especies conocidas. Estos datos genómicos, analizados con métodos basados en coalescencia y redes filogenéticas, revelaron numerosos casos de especiación rápida donde los arboles de genes individuales conflictúan con el árbol de especies. Además, la historia evolutiva de las serpientes de cascabel esta dominada por una especiación incompleta y una frecuente hibridación, las cuales probablemente han influenciado interpretaciones pasadas de las filogenias. Nosotros presentamos un nuevo marco en el que las relaciones evolutivas de este grupo solo pueden ser entendidas en base a datos de genomicos y métodos analíticos basados en redes filogenéticas. Nuestros datos sugieren que la radiación en redes filogenéticas, como se ha visto dentro de las serpientes de cascabel, solo puede ser entendida en un contexto filogenómico, necesitando aproximaciones similares en nuestro intento de entender la historia evolutiva en otras especies con radiaciones rápidas.</p>
Supplementary of Bayesian Evaluation of Incomplete Fission Yields
<p>This part employ a code to read parameters of the trained Bayesian neural network which are stored in the log file, and output the averaged function values and Confidence Interval (CI) of fission yields. The instructions are given in the attached BNN-fission.PDF file. </p> <p> </p>
Data from: Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae)
Hybridization is a frequent and important force in plant evolution. Next-generation sequencing (NGS) methods offer new possibilities for clade resolution and ambitious sampling of gene genealogies, yet difficulty remains in detecting deep reticulation events using currently available methods. We reconstructed the phylogeny of diploid representatives of Amaryllidaceae tribe Hippeastreae to test the hypothesis of ancient hybridizations preceding the radiation of its major subclade, Hippeastrinae. Through hybrid enrichment of DNA libraries and NGS, we obtained data for 18 nuclear loci through a curated assembly approach and nearly complete plastid genomes for 35 ingroup taxa plus 5 outgroups. Additionally, we obtained alignments for 39 loci through an automated assembly algorithm. These data were analyzed with diverse phylogenetic methods, including concatenation, coalescence-based species tree estimation, Bayesian concordance analysis, and network reconstructions, to provide insights into the evolutionary relationships of Hippeastreae. Causes for gene tree heterogeneity and cytonuclear discordance were examined through a Bayesian posterior predictive approach (JML) and coalescent simulations. Two major clades were found, Hippeastrinae and Traubiinae, as previously reported. Our results suggest the presence of two major nuclear lineages in Hippeastrinae characterized by different chromosome numbers: 1) Tocantinia and Hippeastrum with 2n = 22, and 2) Eithea, Habranthus, Rhodophiala, and Zephyranthes mostly with 2n = 12, 14, and 18. Strong cytonuclear discordance was confirmed in Hippeastrinae, and a network scenario with at least six hybridization events is proposed to reconcile nuclear and plastid signals, along a backbone that may also have been affected by incomplete lineage sorting at the base of each major subclade.
Measuring phylogenetic information of incomplete sequence data
<p>Widely used approaches for extracting phylogenetic information from aligned sets of molecular sequences rely upon probabilistic models of nucleotide substitution or amino-acid replacement. The phylogenetic information that can be extracted depends on the number of columns in the sequence alignment and will be decreased when the alignment contains gaps due to insertion or deletion events. Motivated by the measurement of information loss, we suggest assessment of the Effective Sequence Length (ESL) of an aligned data set. The ESL can differ from the actual number of columns in a sequence alignment because of the presence of alignment gaps. Furthermore, the estimation of phylogenetic information is affected by model misspecification. Inevitably, the actual process of molecular evolution differs from the probabilistic models employed to describe this process. This disparity means the amount of phylogenetic information in an actual sequence alignment will differ from the amount in a simulated data set, which motivated us to develop a new test for model adequacy. Via theory and empirical data analysis, we show how to disentangle the effects of gaps and model misspecification. By comparing the Fisher information of actual and simulated sequences, we identify which alignment sites and tree branches are most affected by gaps and model misspecification.</p>
Raw Data for the article: Clinical Insights to Complete and Incomplete Surgical Revascularization in Atrial Fibrillation and Multivessel Coronary Disease
<p><strong>Objectives: </strong>Although endorsed by international guidelines, complete revascularization (CR) with Coronary Artery Bypass Grafting (CABG) remains underused. In higher-risk patients such as those with pre-operative atrial fibrillation (AF), the effects of CR are not well studied.</p> <p><strong>Methods: </strong>We analyzed patients' data from the HEIST (HEart surgery In AF and Supraventricular Tachycardia) registry. Between 2012 and 2020 we identified 4770 patients with pre-operative AF and multivessel coronary artery disease who underwent isolated CABG. We divided the cohort according to the completeness of the revascularization and used propensity score matching (PSM) to minimize differences between baseline characteristics. The primary endpoint was all-cause mortality.</p> <p><strong>Results: </strong>Median follow-up was 4.7 years [interquartile range (IQR) 2.3-6.9]. PSM resulted in 1,009 pairs of complete and incomplete revascularization. Number of distal anastomoses varied, accounting for 3.0 + -0.6 vs. 1.7 + -0.6, respectively. Although early (< 24 h) and 30-day post-operative mortalities were not statistically different between non-CR and CR patients [Odds Ratio (OR) and 95% Confidence Intervals (CIs): 1.34 (0.46-3.86); <em>P</em> = 0.593, Hazard Ratio (HR) and 95% CIs: 0.88 (0.59-1.32); <em>P</em> = 0.542, respectively] the long term mortality was nearly 20% lower in the CR cohort [HR (95% CIs) 0.83 (0.71-0.96); <em>P</em> = 0.011]. This benefit was sustained throughout subgroup analyses, yet most accentuated in low-risk patients (younger i.e., < 70 year old, with a EuroSCORE II < 2%, non-diabetic) and when off-pump CABG was performed.</p> <p><strong>Conclusion: </strong>Complete revascularization in patients with pre-operative AF is safe and associated with improved survival. Particular survival benefit with CR was observed in low-risk patients undergoing off-pump CABG.</p>
Incomplete partitioning of pollinators by Linum suffruticosum and its co-flowering congeners
<p>Data used in the manuscript "Incomplete partitioning of pollinators by <em>Linum suffruticosum</em> and its co-flowering congeners" accepted for publication in American Journal of Botany</p> <p>flower_morphology.csv includes measurements of floral traits</p> <p>Natural_pollen_arrival.csv includes data on pollen arrival on the stigmas and formation of pollen tubes of <em>L. suffruticosum</em> in sympatric and allopatric populations in the Central Pyrenees in Spain and SW Spain</p> <p>Lnarbonense_heterospecific_pollination.csc, Lviscosum_heterospecific_pollination.csv and Ltenue_heterospecific_pollination.csv correspond to the hand-pollination experiments using <em>L. narbonense, L. viscosum </em>and <em>L. tenue</em> as heterospecific pollen donors</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.